BidomainDg0Assembler.hpp

/*

Copyright (C) University of Oxford, 2005-2009

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/


#ifndef _BIDOMAINDG0ASSEMBLER_HPP_
#define _BIDOMAINDG0ASSEMBLER_HPP_

#include "UblasIncludes.hpp"

//#include <iostream>
#include <vector>
#include <petscvec.h>

#include "AbstractDynamicAssemblerMixin.hpp"
#include "AbstractLinearAssembler.hpp"

#include "BidomainPde.hpp"
#include "HeartConfig.hpp"
#include "Element.hpp"
#include "BoundaryElement.hpp"
#include "ChastePoint.hpp"
#include "AbstractMesh.hpp"
#include "BoundaryConditionsContainer.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class BidomainDg0Assembler
    : public AbstractLinearAssembler<ELEMENT_DIM, SPACE_DIM, 2, false, BidomainDg0Assembler<ELEMENT_DIM, SPACE_DIM> >,
      public AbstractDynamicAssemblerMixin<ELEMENT_DIM, SPACE_DIM, 2>
{
public:
    static const unsigned E_DIM = ELEMENT_DIM;
    static const unsigned S_DIM = SPACE_DIM;
    static const unsigned P_DIM = 2u;

protected:
    // Save typing
    typedef BidomainDg0Assembler<ELEMENT_DIM, SPACE_DIM> SelfType;
    typedef AbstractLinearAssembler<ELEMENT_DIM, SPACE_DIM, 2, false, SelfType> BaseClassType;

    friend class AbstractStaticAssembler<ELEMENT_DIM, SPACE_DIM, 2, false, SelfType>;

    BidomainPde<SPACE_DIM>* mpBidomainPde;

    HeartConfig* mpConfig;

    // quantities to be interpolated
    double mIionic;
    double mIIntracellularStimulus;
    double mIExtracellularStimulus;

    bool mNullSpaceCreated;

    Vec mExternalVoltageMask;
    std::vector<unsigned> mFixedExtracellularPotentialNodes;

    unsigned mRowForAverageOfPhiZeroed;

    void ResetInterpolatedQuantities( void );

    void InitialiseForSolve(Vec initialSolution);

    void IncrementInterpolatedQuantities(double phi_i, const Node<SPACE_DIM>* pNode);

    virtual c_matrix<double,2*(ELEMENT_DIM+1),2*(ELEMENT_DIM+1)> ComputeMatrixTerm(
        c_vector<double, ELEMENT_DIM+1> &rPhi,
        c_matrix<double, ELEMENT_DIM, ELEMENT_DIM+1> &rGradPhi,
        ChastePoint<SPACE_DIM> &rX,
        c_vector<double,2> &u,
        c_matrix<double, 2, SPACE_DIM> &rGradU /* not used */,
        Element<ELEMENT_DIM,SPACE_DIM>* pElement);

    virtual c_vector<double,2*(ELEMENT_DIM+1)> ComputeVectorTerm(
        c_vector<double, ELEMENT_DIM+1> &rPhi,
        c_matrix<double, ELEMENT_DIM, ELEMENT_DIM+1> &rGradPhi,
        ChastePoint<SPACE_DIM> &rX,
        c_vector<double,2> &u,
        c_matrix<double, 2, SPACE_DIM> &rGradU /* not used */,
        Element<ELEMENT_DIM,SPACE_DIM>* pElement);

#define COVERAGE_IGNORE //see NOTE above
    virtual c_vector<double, 2*ELEMENT_DIM> ComputeVectorSurfaceTerm(
        const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM> &rSurfaceElement,
        c_vector<double,ELEMENT_DIM> &rPhi,
        ChastePoint<SPACE_DIM> &rX);
#undef COVERAGE_IGNORE

    virtual void PrepareForAssembleSystem(Vec currentSolution, double time);

    virtual void FinaliseAssembleSystem(Vec currentSolution, double currentTime);


public:

    BidomainDg0Assembler(AbstractMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
                         BidomainPde<SPACE_DIM>* pPde,
                         BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, 2>* pBcc,
                         unsigned numQuadPoints = 2);

    ~BidomainDg0Assembler();

    void SetFixedExtracellularPotentialNodes(std::vector<unsigned> fixedExtracellularPotentialNodes);

    void SetRowForAverageOfPhiZeroed(unsigned rowMeanPhiEZero);
};

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
struct AssemblerTraits<BidomainDg0Assembler<ELEMENT_DIM, SPACE_DIM> >
{
    typedef BidomainDg0Assembler<ELEMENT_DIM, SPACE_DIM> CVT_CLS;
    typedef BidomainDg0Assembler<ELEMENT_DIM, SPACE_DIM> CMT_CLS;
    typedef BidomainDg0Assembler<ELEMENT_DIM, SPACE_DIM> INTERPOLATE_CLS;
};

#endif /*_BIDOMAINDG0ASSEMBLER_HPP_*/

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